Download the package in these google links for [https://drive.google.com/open?id=1hdYLVsoqEQAbP7CdUxCpdUjrBtDAm1i2 Mac], Windows or [https://drive.google.com/open?id=1lkm1pEFC2HahvUYGIgYdjDzoDhLfJb0k Linux]. After download (~4Gb), proceed to [[Installation | install and test]]

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Download the package in these google links for [https://drive.google.com/open?id=1hdYLVsoqEQAbP7CdUxCpdUjrBtDAm1i2 Mac], Windows or [https://drive.google.com/open?id=1lkm1pEFC2HahvUYGIgYdjDzoDhLfJb0k Linux].

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=== Installation ===

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==== Linux and Mac ====

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After download (~4Gb), proceed to [[Installation | install and test]]

To install it, first create a folder in your filesystem in an arbitrary location of your choice:

To install it, first create a folder in your filesystem in an arbitrary location of your choice:

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<tt>tar -xf <tar file> -C <path to installation folder></tt>

<tt>tar -xf <tar file> -C <path to installation folder></tt>

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==== Windows ====

For Windows platforms, we provide a zip file, that can be installed likewise.

For Windows platforms, we provide a zip file, that can be installed likewise.

Revision as of 16:51, 26 January 2018

This page describes the contents of the practical hands-on sessions of the Dynamo UCSD workshop (29th-30th January 2018).

Preinstalling the software

Participants are asked to bring their own laptops. We will reserve the first hour before the workshop to proceed to installation and troubleshooting on all the individual laptops.
However, we strongly encourage participants to install and test the Dynamo software beforehand using the instructions below. Links to the Dynamo version that will be used during the workshop will be updated on the Friday, 26th of January.

We suggest students to download, install and test the software before departing for the workshop. Data should also be downloaded beforehand. Also note that you might need admin privileges to complete the steps below in some platforms. Make sure that you have access to admin credentials on your laptop.

You can use Dynamo with or without Matlab (standalone modus). Both options are fine to follow the contents of the workshop. We advice you to use it under Matlab, at the price of a slightly more complicated installation procedure.

Downloading Dynamo

Installation

Linux and Mac

To install it, first create a folder in your filesystem in an arbitrary location of your choice:

mkdir <path to installation folder>

and untar the downloaded tarball into it:

tar -xf <tar file> -C <path to installation folder>

Windows

For Windows platforms, we provide a zip file, that can be installed likewise.

Testing your standalone installation

We will first test if the package that you just downloaded and untarred/unzipped is functional on your system. This involves first activatingDynamo in a terminal, and then running it.

Activate shell in Mac/Linux

Activate your installation to work in standalone modus by typing in a Linux/MacOS shell the activation script:

source <path to installation>/dynamo_activate_linux_shippedMCR.sh

or correspondingly for Mac:

source <path to installation>/dynamo_activate_mac_shippedMCR.sh

Activate terminal in Windows

On a command prompt, type:

<path to installation>/dynamo_activate_windows.bat

Start Dynamo(all platforms )

From this point on, all platforms will work likewise. To test the activated installation, just type in the terminal:

dynamo

You should get the standalone Dynamo prompt in your terminal:

Dynamo >

It might take some time till it is operative (between seconds and minutes).

Free license for Matlab

If the standalone installation works, you don't need to install further elements in your system. You will be able to follow the contents of the workshop. However, we advice you to preinstall Matlab on your laptop. This makes the work with Dynamo much more comfortable.

You can get a trial version of Matlab and install it on your laptop. The license will be valid for 30 days. After installing Matlab, you can download the Dynamo version for your platform.

Testing your Matlab installation

Inside the Matlab shell type:

run <path to installation>/dynamo_activate.m

Virtual machines

We recommend to use this device only as a last resource.
If your system does not recognize the libraries provided in your package, you always have the option of installing a Virtual Machine in your system that emulates the Ubuntu distribution of linux. In this environment, Dynamo will run without errors, although the performance of the graphics system will be severely decreased.

Preparing your Matlab in Windows

If the standalone fails, a Matlab trial version should be used. Please download it from Mathworks.
In order to check if your system has all the libraries needed to run Dynamo, write in the Matlab shell

run <path to installation>/dynamo_activate.m

If the activation fails, you need to compile (i.e. 'mex') some files. These requieres to have a compiler on your system. Write

mex -setup

in the Matlab shell.

Installing a C++ compiler for windows

This will direct you to install a c++ compiler specific for the Matlab-Windows (MinGW-w64). You just need to follow the instructions on screen. Should take less than three minutes.

When the compiler is installed, run

mex -setup

to check that the system recognizes it. Then run dynamo_activate.m again.

Data

Downloading data beforehand may help avoiding waiting time during the workshop.

Template matching

Adaptive bandpass filtering

Working on your own:

We will follow this walkthrough to create a small synthetic data set that illustrates the principles of adaptive bandpass filtering, a way of conducting a golden standard alignment procedure . (~40 mins)